19-43673836-T-G

Position:

• chr19-43673836-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.576 in 151,940 control chromosomes in the GnomAD database, including 25,387 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25387 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43673836T>G		intergenic_region
LOC124904724	XR_007067264.1	n.875+3356T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87395 AN: 151822 Hom.: 25363 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.588

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.576 AC: 87474 AN: 151940 Hom.: 25387 Cov.: 32 AF XY: 0.572 AC XY: 42484 AN XY: 74246

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.590

Alfa AF: 0.600 Hom.: 9013

Bravo AF: 0.569

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs344779; hg19: chr19-44177988;